- It adds a suffix to project name, something like "App(22)", no way to rename it.
- It doesn't have npm / bower / grunt tooling (similar how you manage NuGet packages in C# projects)
- No way to define where you have source code, tests etc, which 3rd party libraries should be available as references (for IntelliSence) in which parts of your code.
- Website project settings are completely irrelevant for typical front-end apps (see yeoman templates)

For complete list of features which would be nice to have in Visual Studio see WebStorm IDE, which is currently better suited for working on front-end projects.

@Adam, I don't think toggling comments functionality works the way you described, rather it works like this - if there are any comment in a selected block they are removed, if not, the block is commented out.

@Jon, schroedl commented about assigning a custom shortcut to an existing command. But, in visual studio there is no such functionality as toggling comments (one command for both commenting and uncommenting). That's the problem!

@schroedl there are no an existing command in Visual Studio for toggling comments (one command for comment/uncomment). Currently you should either use ReSharper for that, or implement a custom macros which will be at least 50 lines of code long (if you need to make it work with different types of comments / files: .css, .cs, .html, .cshtml etc.)